Friday, July 1, 2011

Recent Log

So here is what is going through recently into my project. I had been able to read a phylogeny. Now I have also completed PhylogenyProcessor. So now I have at hand a drawable phylogeny.

The parent nodes have been assigned the mean coordinates of their children. I am thinking to modify it to a weighted average so that the length of the edges correspond to the time span.
If clades are specified then each clade is assigned a new random color. Any parent node's color is the arithmetic mean of the colors of its children.

The code is up on github so you can have a look at it.

My current efforts are directed in coding the KmlWriter classes that will draw the phylogeny onto the kml. Presenting 4000 nodes all at once leads to clutter and chaos on the map. I am thinking of ways to prevent such a catastrophe. Ideas are welcome !
Some ideas I had are as follows.

Build each level of the tree into a separate folder, this way user can select what stuff he wants to see and what he/she does not want to.

The second was to display it cladewise. But this seems to be a futile idea because the cocept of clade begins to fade out as we move up the tree. So the HTU's belong to which clades when their children belong to different clades is indeed a vague question. So I have dropped this idea.

The third is to put the placemarks in the map at various different levels in the map.